Trends in Population Dynamics of<i>Escherichia coli</i>Sequence Type 131, Calgary, Alberta, Canada, 2006–20161
Bibliographic record
Abstract
E scherichia coli sequence type (ST) 131 is the quint- essential example of a successful, global, antimicrobial-resistant, high-risk clone among human bacteria (1,2).Currently, ST131 is the most common global extraintestinal pathogenic E. coli (ExPEC) clone; up to 30% of all ExPEC, 60%-90% of fluoroquinolone-resistant ExPEC, and 40%-80% of ExPEC with extended-spectrum β-lactamases [ESBLs] belong to ST131 (3,4).Population genetics indicate that ST131 consists of different clades (5): clade A contains serotype O16:H5 and fimH41, clade B contains mostly serotype O25b:H4 and fimH22, and clade C contains serotype O25b:H4 and fimH30.Clade C is divided into 2 subclades: C1/H30R (associated with fluoroquinolone resistance) and C2/H30Rx (associated with fluoroquinolone resistance and bla CTX-M-15 ).A novel ST131 C1 subclade, known as C1-M27 with bla CTX-M-27 , was reported in Japan (6).ST131 is the most dominant and most antimicrobial-resistant among E. coli causing bloodstream infections in Calgary, Alberta, Canada, infecting mostly the elderly in long-term care centers (7).Previous molecular epidemiology studies from the same region showed that ST131 was relatively rare among ESBL-producing and fluoroquinoloneresistant E. coli during the early 2000s but showed a major increase toward the end of the 2000s (8,9).However, limited information is available regarding the changes in population dynamics of ST131 clades over extended periods, especially among nonbiased E. coli isolates in large, well-defined, geographic regions.To address this issue, we conducted a retrospective cohort study that characterized ST131 clades responsible for bloodstream infections in Calgary over an 11-year period (2006-2016).Investigating trends of ST131 clades over long periods by using a populationbased surveillance approach will aid in clarifying the evolution of this clone and help with designing superior prevention strategies (3,10).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".